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Update computeGibbsFreeEnergyRanges.m #131

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73 changes: 64 additions & 9 deletions matlab_code/ensembleFxns/computeGibbsFreeEnergyRanges.m
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Original file line number Diff line number Diff line change
Expand Up @@ -57,19 +57,74 @@
Sthermo = ensemble.Sthermo;
Sflux = ensemble.Sflux;

DGf_std_max = pinv(Sthermo*Sthermo')*Sthermo*DGr_std_max;
DGf_std_min = pinv(Sthermo*Sthermo')*Sthermo*DGr_std_min;
for ix = 1:numel(DGf_std_max)
if (DGf_std_min(ix)>DGf_std_max(ix))
DGf_std_temp = DGf_std_max(ix);
DGf_std_max(ix) = DGf_std_min(ix);
DGf_std_min(ix) = DGf_std_temp;
% First we estimate feasible ranges for DGf_std from DGr_std_max. This is
% done solving various LP problems to ensure consistency
[m,n] = size(Sthermo);
[~,nflux] = size(Sflux);
M = 1e3;
DGf_std_min = zeros(m,1);
DGf_std_max = zeros(m,1);

if strcmp(ensemble.LPSolver, 'gurobi')

gurobiModel.A = sparse([eye(n),-Sthermo']);
gurobiModel.rhs = zeros(n,1);
gurobiModel.lb = [DGr_std_min(:);-M*ones(m,1)]; % Only negative DGf_std
gurobiModel.ub = [DGr_std_max(:);zeros(m,1)];
gurobiModel.obj = zeros(m+n,1);
gurobiModel.sense = '='; % Constraint type definition
gurobiModel.vtype = 'C'; % Variable type definition

% Define optimization parameters
params.outputflag = 0;
params.FeasibilityTol = 1e-9;
params.OptimalityTol = 1e-9;

% Find feasible ranges for each DGf_std
for ix = 1:m
gurobiModel.obj(n+ix) = 1;
gurobiModel.modelsense = 'min';
solmin = gurobi(gurobiModel,params);
DGf_std_min(ix) = solmin.objval;

gurobiModel.modelsense = 'max';
solmax = gurobi(gurobiModel,params);
DGf_std_max(ix) = solmax.objval;
gurobiModel.obj(n+ix) = 0;
end

elseif strcmp(ensemble.LPSolver, 'linprog')

A = [];
b = [];
Aeq = [eye(n),-Sthermo'];
beq = zeros(n,1);
lb = [DGr_std_min(:);-M*ones(m,1)];
ub = [DGr_std_max(:);zeros(m,1)];
x0 = [];
fobj = zeros(m+n,1);

options = optimoptions(@linprog, ...
'OptimalityTolerance', 1e-9, ...
'ConstraintTolerance', 1e-9, ...
'Display', 'off');

% Find feasible ranges for each DGf_std
for ix = 1:m
fobj(n+ix) = 1;
[~,fval] = linprog(fobj, A, b, Aeq, beq, lb, ub, x0, options);
DGf_std_min(ix) = fval;
fobj(n+ix) = -1;
[~,fval] = linprog(fobj, A, b, Aeq, beq, lb, ub, x0, options);
DGf_std_max(ix) = -fval;
fobj(n+ix) = 1;
end

end


% Build the adapted TMFA problem
K = 1e12;
K = 1e12;
delta = 1e-6;
RT = 8.314*298.15/1e3; % [kJ/mol]
M = 1e5;
Expand Down Expand Up @@ -303,4 +358,4 @@
end
end

end
end